I had the same creaking on my '98. Their are 2 components to each door a glide and 2 hinges. I at first tried some silicon spray lubricant on the glide bar which did not fix the problem. Next I used #2 Lithium grease on the glide rails, put it on nice and thick and worked it in by opening and closing the door. After a few days the creak was gone I think some flex in the chassis while driving really drove the grease into where it was creaking. I also sprayed silicon lube on the hinge points. I have been creak free for over a year. Hope that helps.

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1998 ML 320
BIG Sound